Originally Posted by The Ancient Geek
Cockpit windshield failure :
This is a possible cause which we have not considered. Such events are rare but they have happened. This would cause explosive cockpit decompression and incapacitation of almost certainly at least one pilot.
With the captain incapacitated and the FO probably injured the shock and startle effect would leave a less experienced FO with a serious workload problem.
Doesn't explain the transponder ceasing all transmissions.